Yes, the longer length of the "Protected" batteries is the exact reason.
Those battery makers are making them longer and longer nowadays completely disregarding the specs.
18650, 16340, etc. used to mean something.
Then they go and slap on protection circuits, charging ports, etc. making them crazy long.
For 18650: 18mm is the diameter of the cell, 65mm is the length of the cell.
For 16340: 16mm is the diameter and 34mm is the length.
The Surefire E Series lights has an internal stepped "lip" at the tailcap side, that means if you use a longer cell it will sit higher.
When you screw the head on with the LED module there is a lot of torque and I have seen the driver crack in half in the worst case.
Most cases is that it causes contact issues with the negative contact not touching the host because the battery is longer and sticking up towards the front end.
The E1e were never meant for those longer cells, so please do not use them.
Cheers.
Mark